Beer Reviews, Homebrew, Rambling

The paper on brewing yeast domestication authored by the Verstrepen lab and White Labs last year is a fantastic piece of work (i.e. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts, Gallone et al. 2016, Cell). I’m sure most of you have seen it by now, so I won’t be going into any details about it. While the article and the work that has been done is amazing, there is one big negative about it: the strains used in the study have been coded, and there is no way of knowing what strain in the paper corresponds to what strain from White Labs or the Verstrepen lab. This means that the readers can’t really benefit from the huge amount of phenotypic data that the study generated. Wouldn’t be nice, for example, to know which White Labs strains are POF+, which ones can’t use maltotriose, which ones produce high concentrations of isoamyl acetate, or which ones sporulate easily?

There is one way of finding out what the coded strains are though, but unfortunately it isn’t completely straight-forward and at the moment it can only be done with a handful of strains. The authors have released the genome assemblies for each of the strains used in the study (available here: https://www.ncbi.nlm.nih.gov/bioproject/323691). The genomes of some White Labs strains have been sequenced in other studies, and performing a search for ‘WLP*’ in the NCBI database yields some hits (https://www.ncbi.nlm.nih.gov/biosample/?term=WLP*). Most of these Illumina reads are from a recent paper focusing on wine yeasts by Borneman et al. 2016. Luckily the strains weren’t coded in this study, and we know what White Labs strains these sequence reads are derived from.

What I then did, was download all of the raw sequence reads for any White Labs strains I could find. I then aligned them to a brewing yeast reference genome (VTT-A81062). After alignment, I looked for SNPs with FreeBayes, and used the resulting VCF files to create consensus sequences for each White Labs strain using BCFtools. I then used ParSNP to perform core genome alignment on these consensus sequences and all 157 of the assemblies from the Gallone et al. paper that I had obtained previously. ParSNP outputs a core genome phylogeny (generated with FastTree2) and a SNP matrix. I additionally produced a maximum likelihood phylogenetic tree using the SNP matrix and ExaML. To identify the White Labs strains from the coded strains in the Gallone et al. paper, I then looked for the closest hits in the phylogenetic tree (this was really obvious for most strains). In cases when there wasn’t one obvious hit, I also looked at Supplementary Table S1 in Gallone et al. 2016 for the reported origin and source of each strain.

Using this approach, I was able to identify eight White Labs strains from the set of coded strains. I know it is not much, but at least it is a good start, and it already gives some interesting and valuable information. First of all here are the results:

The question mark (?) after the ‘Code in paper’ means that there were two close hits, and I chose the match based on the reported origin and source as well. First of all, my suspicions regarding WLP099 were true (see this old post), with it being Beer033, a yeast grouping in the wine clade and unable to use maltotriose. Interestingly, WLP570 (Beer085) also seems to be unable to use maltotriose. This should be the ‘Duvel’ strain, and based on this information, it should only be able to produce bone-dry beers in worts supplemented with sugars (as Duvel is, if I’ve understood correctly). Another interesting observation we can make is that WLP705 appears to be Sake002. This is the only out of the seven Sake strains that wasn’t grouped in the Asian clade, but rather in the wine clade. Is this really a Sake yeast, or is it a mislabeled wine yeast? Anyways, there is a lot of interesting data to be extracted from these strains alone (esters, ethanol tolerance, etc.)!

While writing this blog post, I also noticed that the authors have released the Illumina reads to all the strains as well (in June 2017 apparently). This should allow me to confirm these results by looking at things such as chromosome copy numbers (through coverage) and SNP heterozygosity (the assemblies are haploid sequences). Unfortunately, I probably won’t have time to do that anytime soon though. But hopefully I can have a look at those later during the winter.

I will also be keeping an eye on the NCBI databases in case more White Labs strains are sequenced in the future!

I feel bad for again having to start off a post by apologizing for my inactivity here at the blog. It has been quite a busy summer for me, as my wife and I got our first child (his name is Ludwig) in the end of June. I’m currently on parental leave from my research work, so have also been busy with wrapping up my ongoing work, so I can continue with it when I return from my leave in March. Anyways, we have been working on lots of interesting hybrid-related projects at our lab, so I thought I’d briefly sum up some of the topics we’ve been working on:

Adaptive evolution of newly created lager hybrids

This is the project I’ve been dedicating most of my time to the past 18 months. While the results haven’t been published in a peer-reviewed journal yet, we’ve submitted a manuscript based on the results for review, and have uploaded a pre-print to bioRxiv for everyone to read. We and others before us, have noticed that many hybrids (particularly interspecies ones) tend to have quite unstable genomes. This means that their genomes, along with their phenotypic properties, can change as the hybrid is grown for several generations. This is not very desirable in a brewing environment, where yeast is reused for multiple consecutive fermentations. We decided to exploit this instability, by growing (and adapting) some of our hybrids in media containing high ethanol concentrations for 130+ generations. We isolated colonies of variant strains along the adaptation process, and through a screening step, we managed to select several variant strains that outperformed the original hybrids in wort fermentations. Many of these variants also had higher ethanol tolerance than the original hybrids, and produced a more desirable aroma profile (more esters, less higher alcohols, and less diacetyl). We sequenced the genomes of these variants, and noticed that all variants had undergone gains and losses of various chromosomes. The results seemed to suggest that the S. cerevisiae sub-genome in the hybrids was ‘preferred’, while the S. eubayanus sub-genome had undergone more losses. We also identified multiple single nucleotide polymorphisms and small indels which affected the coding sequence of many genes. Mutations in some of these genes had previously been reported to affect ethanol tolerance and general fitness. In addition, these variant strains appeared stable when grown for multiple generations. All in all, our study shows that interspecific hybridization, coupled with adaptive evolution, is a powerful tool for producing new strains with tailor-designed properties.

This is a project a MSc student, Jarkko Nikulin, worked on last year. We wanted to investigate whether S. eubayanus really is that important for lager (i.e. low-temperature) fermentations. Studies have shown that there are several other cold-tolerant Saccharomyces species (though not as cold-tolerant as S. eubayanus), and the questions was: can we replace S. eubayanus in a lager hybrid with one of these alternative Saccharomyces species? We generated a range of S. cerevisiae × (S. arboricola / S. eubayanus / S. mikatae / S. uvarum) hybrids and compared them in wort fermentations. We noticed that S. eubayanus seems to be dispensable, as many of the other alternative hybrids performed just as well in low-temperature wort fermentations. There is a quite a lot of potential to generate some really diverse and unique strains using these alternative Saccharomyces species.

This is a project my colleague and fellow PhD student Frederico Magalhaes has been working on. In his PhD project he has been looking at the use of S. eubayanus for cider and wine-making. Many wine fermentations are carried out at lower temperatures, e.g. to increase aromatic complexity and decrease the growth of contaminants, and the use of S. eubayanus would allow for that. You can read more about Frederico’s work in the following blog post:

Finally, here is a review on modern brewing yeast design and development that I was involved in, and was written for the ISSY33 conference that took place this summer in Ireland. Some of the topics that are covered are non-conventional brewing yeast, hybridization and genome analysis.

The title of this post may sound a little confusing or complex for those not familiar with the nomenclature of the field, but I’ll try my best to explain our recent results to you. As I’ve written many times previously on this blog ([1], [2], [3], [4], and [5]), I have been working with and researching yeast hybrids and their use in brewing for my PhD thesis. I’ve been focusing especially on lager yeast hybrids, i.e. Saccharomyces cerevisiae × Saccharomyces eubayanus. Research, both our own and in other labs, has shown that generating new lager yeast hybrids by breeding strains of S. cerevisiae with S. eubayanus is possible, and that these new hybrids often possess desirable properties compared to the parent strains. These properties include improved fermentation rate, better stress tolerance and a more diverse formation of aroma compounds. However, one trait that has been plaguing all de novo lager yeast hybrids, is their inherent tendency to produce phenolic off-flavours (POF, i.e. the spicy, clove-like aroma that is characteristic of wheat beers and Belgian-style beers). This is an undesirable trait that is inherited from the Saccharomyces eubayanus parent. It doesn’t matter if the other parent produces phenolic off-flavours or not, the de novo lager hybrid will always produce it, as it inherits the relevant genes (more on this below) from the S. eubayanus parent. So with this in mind, and the idea that it would be cool if you could combine properties from more than two parent strains into a hybrid, we started thinking and experimenting.

One way that it is possible to remove unwanted traits from a yeast strain, is through sporulation and meiotic recombination (note, this only works if the strain is heterozygous at the loci responsible for the trait). Sporulation would also give us the opportunity to add in features from a third parent strain, as one could mate the hybrid spore clone (having a single mating type) with a third parent strain. However, interspecies hybrids tend to be sterile (this is also true for animal hybrids such as mules or ligers), which means that they don’t form any viable spores. Therefore, one would think that this is an impossible route to go down. What is interesting though, is that studies have shown that sterility mainly afflicts allodiploid hybrids (i.e. the hybrid has inherited one copy of each chromosome from both parents, just like us humans), and that allotetraploid hybrids (i.e. the hybrid has inherited both copies of each chromosome from both parents) tend to remain fertile. With this in mind, we constructed a set of five hybrids from three parents. Two of these hybrids contained DNA from all three parent strains, and from one of these two hybrids we successfully removed POF formation. These hybrids were constructed with fertile allotetraploid intermediates (which were capable of efficient sporulation) using the following scheme:

Before I get into the properties of this set of eight strains, I’ll quickly go through the cause of the ‘POF phenotype’. Many strains of Saccharomyces produce vinyl phenols from hydroxycinnamic acids, and these phenolic compounds are considered undesirable in many beer types (especially lager beer). The most well-studied of these vinyl phenols is 4-vinyl guaiacol, which is formed from ferulic acid. We know, thanks to work by Mukai et al., that the ability of brewing yeast to produce volatile phenols is attributed to the adjacent PAD1 and FDC1 genes, both of which are needed for a POF+ phenotype. Wild yeast strains, such as S. eubayanus, tend to have functional PAD1 and FDC1 genes, while domesticated POF- brewing yeast have nonsense or frameshift mutations in these genes, making them non-functional (e.g. see the recent Gallone et al. paper in Cell). The biological function of this mechanism is to protect the cell from the toxic effects of hydroxycinnamic acids (mainly plants produce them as antibiotics), which is why one can expect to find only POF- strains among domesticated yeasts. So if any non-functional alleles of PAD1 or FDC1 are present in the hybrid genome, it should be possible to remove the POF+ phenotype through meiotic recombination (as we demonstrate).

For this set of eight strains, we began with three parent strains (P1-P3). Two of them are S. cerevisiae ale strains (P1: VTT-A81062, P2: WLP099) and one is the S. eubayanus type strain (P3: VTT-C12902). These strains were chosen for their varying properties. Of the three, P1 is the only strain that is able to use maltotriose during fermentation, P2 is the only strain that does not produce 4-vinyl guaiacol (i.e. it is POF-), while P3 is the cold-tolerant parent strain of lager yeast. We began by creating the three possible double hybrids (P1 × P2, P1 × P3, P2 × P3) through rare mating. Hybrid H1 (P1 × P3) was fertile (thanks to allotetraploidy), despite it being an interspecific hybrid, and it produced viable spores efficiently. So we sporulated Hybrid H1 and then mated a mixture of its spores with parent strain P2 to obtain the triple Hybrid T1 ((P1 × P3) × P2). Whole genome sequencing revealed that the sub-genome ratio in T1 was approximately 1:2:1 (P1:P2:P3). Hybrid T1 was also an allotetraploid and it was able to form viable spores. Knowing that the genome contained both functional and non-functional alleles of PAD1, we attempted to remove the POF+ phenotype from Hybrid T1 through sporulation according to the image below. What we did was sporulate Hybrid T1, isolate individual spore clones, and then screen them for the POF phenotype in media containing ferulic acid. POF+ spore clones would produce a strong clove-like aroma in the media, while POF- spore clones would not. Approximately 25% of the spore clones were POF− (as one would expect), and the best growing of these was given the name Hybrid T2, i.e. a POF− meiotic segregant of Hybrid T1.

We wanted to compare how these 8 brewing strains would perform in wort fermentations at lager brewing conditions (15 °P all-malt wort at 15 °C). There was considerable variation in fermentation performance between the eight strains, as you can see in the figure below (A). Of the 8 strains, Hybrid T1 and S. cerevisiae P2 had the highest overall fermentation rates, but these slowed down considerably after reaching 5.8% (v/v) alcohol. We looked at the sugars present in the beer, and saw that S. cerevisiae P2 was unable to ferment the maltotriose in the wort (D). Hybrid T1 had only consumed a small amount of the initial maltotriose present in the wort (D). Of the 8 strains, Hybrid T2 attenuated the best, followed closely by Hybrids H1 and H3 (A). These three hybrids had also used maltotriose efficiently (D). The beers produced with the 8 brewing strains also varied considerably in concentrations of aroma-active compounds (B). The most ester-rich (i.e. fruity) beers were produced with Hybrids H1, H3 and T1. When we compare the aroma profiles of the beers made with Hybrids T1 and T2, we see that the meiotic segregant T2 produced lower concentrations of most esters, while its beer contained higher concentrations of most higher alcohols. This could maybe be explained by it having lower activities or expression of alcohol acetyl transferases (e.g. ATF1 and ATF2). Of the 8 strains, the POF− S. cerevisiae P2 parent strain and Hybrid T2 were the only ones that did not produce any detectable amounts of 4-vinyl guaiacol (detection limit 0.2 mg L−1), thus confirming their POF− phenotype (C). All other strains produced 4-vinyl guaiacol in concentrations above the flavour threshold of 0.3–0.5 mg L−1. We finally compared the sequences of PAD1 and FDC1 in the 8strains, and found that Hybrid T2 only carried the PAD1 allele that was derived from S. cerevisiae P2 (E). This particular allele, contained a possible loss-of-function SNP at position 638 (A>G, resulting in an amino acid substitution of aspartate to glycine). The other strains, including Hybrid T1, which Hybrid T2 was derived from, carried either or both of the functional PAD1 alleles derived from S. cerevisiae P1 or S. eubayanus P3.

So there you have it, some cool things you can do with allotetraploid interspecific hybrids. We wanted to demonstrate that it is possible to construct complex yeast hybrids that possess traits that are relevant to industrial lager beer fermentation and that are derived from several parent strains. If you are interested in some more info on the topic (e.g. some lipidomics analysis of these strains), I’m happy to announce that an article based on these results was recently published in Microbial Cell Factories:

Please feel free to check it out (it is open access)! Here is the abstract:

Abstract

Background

Interspecific hybridization has proven to be a potentially valuable technique for generating de novo lager yeast strains that possess diverse and improved traits compared to their parent strains. To further enhance the value of hybridization for strain development, it would be desirable to combine phenotypic traits from more than two parent strains, as well as remove unwanted traits from hybrids. One such trait, that has limited the industrial use of de novo lager yeast hybrids, is their inherent tendency to produce phenolic off-flavours; an undesirable trait inherited from the Saccharomyces eubayanus parent. Trait removal and the addition of traits from a third strain could be achieved through sporulation and meiotic recombination or further mating. However, interspecies hybrids tend to be sterile, which impedes this opportunity.

Results

Here we generated a set of five hybrids from three different parent strains, two of which contained DNA from all three parent strains. These hybrids were constructed with fertile allotetraploid intermediates, which were capable of efficient sporulation. We used these eight brewing strains to examine two brewing-relevant phenotypes: stress tolerance and phenolic off-flavour formation. Lipidomics and multivariate analysis revealed links between several lipid species and the ability to ferment in low temperatures and high ethanol concentrations. Unsaturated fatty acids, such as oleic acid, and ergosterol were shown to positively influence growth at high ethanol concentrations. The ability to produce phenolic off-flavours was also successfully removed from one of the hybrids, Hybrid T2, through meiotic segregation. The potential application of these strains in industrial fermentations was demonstrated in wort fermentations, which revealed that the meiotic segregant Hybrid T2 not only didn’t produce any phenolic off-flavours, but also reached the highest ethanol concentration and consumed the most maltotriose.

Conclusions

Our study demonstrates the possibility of constructing complex yeast hybrids that possess traits that are relevant to industrial lager beer fermentation and that are derived from several parent strains. Yeast lipid composition was also shown to have a central role in determining ethanol and cold tolerance in brewing strains.

I’m not the biggest fan of sour beer, but I am still very interested in brewing with non-conventional microbes. I brewed a batch of sour beer using Wyeast’s Lambic Blend and some bottle dregs around 3.5 years ago. It turned out surprisingly nice, and it got complements from many of my friends who love sour beer. Together with one of these friends, I brewed up a fresh 30L batch of wort (a couple of weeks ago), which I split into two fermenters. These two sub-batches were pitched with two different cultures: The Yeast Bay’s House Sour Blend, which contains a mixture of several different yeasts and bacteria, and a pure culture of a strain of Lachancea thermotolerans, which we’ve (our lab at VTT) isolated from an oak tree here in Finland.

Lachancea thermotolerans is a very interesting yeast, because of its ability to produce lactic acid. From a brewing perspective, this means it can applied e.g. to sour beer production. This is particularly interesting, because it allows for the production of sour beer without the cross-contamination risks associated with the use of lactic acid bacteria. Lachancea thermotolerans has recently gathered some interest in the brewing science community as well, as last year there were some published studies and conference presentations on the topic.

We haven’t really characterized our isolate of L. thermotolerans yet, so I thought I’d try it out in a homebrew batch. The pre-culture was smelling promising, with a strong fruity aroma combined with a distinct lactic tartness. As I wasn’t sure how the isolate would handle high osmotic stress or high ethanol concentrations, we decide to play it safe by brewing a relatively low-gravity wort. Using a 50/50 blend of pale ale malt and wheat malt, we aimed for a specific gravity of 1.050. As my brew kettle doesn’t fit 30 liters of wort, we decided to dilute the ‘Sour Blend’ portion of the wort with water. Hence we ended up with 15 liters of 1.049 wort for the L. thermotolerans portion, and 15 liters of 1.037 wort for the ‘Sour Blend’ portion.

For hops, we went with some old Saaz hops from 2010 I found in the freezer. We only aimed for a couple of IBUs. The L. thermotolerans portion got an additional handful of Nelson Sauvin hops I also found in the freezer (from 2013, so it had definitely lost some punch) added to it after flameout. We were hoping this would complement the fruity aroma that the yeast seems to produce and add a slight bit of extra bitterness.

After 2 weeks of fermentation (starting from around 19C, rising to around 23C), I transferred the L. thermotolerans portion to a keg for carbonation. The gravity had dropped to 1.011 (for an attenuation of around 78%), suggesting the yeast is capable of using maltotriose. This is quite an important result, as maltotriose is typically the second most abundant sugar in wort. The pH of the beer had dropped to 3.48 and the beer was definitely tasting sour, suggesting that a considerable amount of lactic acid had been produced by the yeast during fermentation.

Overall I’m very happy with the flavour and the aroma. The aroma is very fruity, with hints of stonefruit and tropical fruits. In the flavor there is a nice balance between the fruity and the sour notes. The flavour is also very clean, and with this I mean that there are no strange or off-putting off-flavours. This L. thermotolerans isolate also doesn’t produce any phenolic off-flavours (POF-).

L. thermotolerans is definitely a promising candidate for sour beer production, and I’m sure we will see more acid-producing yeasts pop up in the near future.

I posted a similar post in the ‘Milk The Funk’ Facebook group recently, and thought I’d copy it over to the blog as well. This post will be about White Labs’ WLP099, which I’ve been using recently for some fermentations. What are people’s experiences with it? Reading around on various homebrew forums etc. you get the impression that this yeast is a monster that will eat through everything you throw at it. Some people are even reporting that it ferments worts down to specific gravities closer to 1.000 (just do a search for “WLP099” on Homebrewtalk). This is very much in contrast to my own experiences with. Using single cell isolates of it in test fermentations, I’ve noticed that it is unable to use maltotriose, and usually ends up with attenuations of around 70% in wort. The only other similar experience I found after googling around was (apparently with input from Mr. White himself):

This of course very much goes against the fact that this yeast could ‘super-attenuate’ plain wort (which would at least require the use of maltotriose, and possibly even longer sugars). So I guess these high attenuations can only be achieved in worts supplemented with simple sugars? Another possibility is that the yeast is actually a blend (either intentional or unintentional; more on this later below).

I did some more digging, and came across this recent study by Borneman et al.:

In it they’ve sequenced a set of mostly wine strains, but they’ve included some White Labs strains as well: one of which is WLP099. Interestingly, it was found to belong to the wine yeast clade. So the fact that it actually seems to be a wine strain, would explain the lack of maltotriose use (and would fit with it having good ethanol tolerance). This paper unfortunately doesn’t go into physiology.

Another study that probably included this strain and does go into physiology is of course the recent Gallone et al. paper:

The strain names are unfortunately encoded, but I did some more digging. Going by the fact that WLP099 is POF-, I looked at the SNPs in the sequences of its PAD1 and FDC1 genes using the reads from the Borneman et al. paper:

Cross-referencing with all the sequences from the Gallone et al. paper, I was able to find only 7 strains containing the same SNPs (Beer024, Beer033, Beer088, Spirits002, Wine001, Wine009 and Wine013); all seven of which belong to the wine clade! Of these strains one, Beer033, seems to have a familiar origin and description (from Table S1): England, Beer (Strong Ale). I think we’ve found WLP099. Anyways, looking at Figure 3 and Table S5 we see that this strain doesn’t use maltotriose! Five of the other six strains which it could be also don’t use maltotriose. Beer088 is the only strain with the same SNPs which uses maltotriose, but its origin is Germany so it’s unlikely that strain would be WLP099.

So, looking at the different independent evidence (my own ferments, the forum post with the apparent input from Chris White, and the Borneman et al. and Gallone et al. papers) it looks like WLP099 is actually a wine strain and I think we can say for sure that it doesn’t use maltotriose and thus won’t super-attenuate in wort, unless it has been supplemented with simple sugars. So regarding finishing off high-gravity ferments with this yeast, it looks like it is only useful for worts to which you add sugar. In worts made only from malt, WLP099 would likely have little to no effect when adding it as a secondary yeast (i.e. when all of the monosaccharides and most of the maltose has been consumed).

So how are peopling still getting 80+% attentuations with WLP099 as the only yeast in all-malt worts? There was some speculation in the ‘Milk The Funk’ Facebook group, that WLP099 might actually (either intentionally or unintentionally) contain two yeast strains (two independent observations were given). If the other yeast strain was a dextrin-degrading one, such as S. cerevisiae var. diastaticus, it could explain how people are seeing ‘super-attenuation’ with WLP099. These strains produce extracellular glucoamylase enzymes which break down dextrin to glucose molecules, which WLP099 could then easily ferment. But this is of course only speculation!

I’m really sorry for not posting in this blog more actively. I haven’t really been homebrewing much the past year, since we moved to a new house that needed renovating. We’ve finally renovated the garage into a brewing space and home bar, so I will hopefully be posting more actively about homebrewing now. I actually even brewed two batches of beer here in the new house last weekend, and I’ll be posting an update of them along with some pictures of the new brewing space in a future post.

Besides homebrewing, I like to write about my own and other’s beer and yeast research on the blog. We have some really interesting yeast projects going on, which I hope to be able to share with you soon. In the meanwhile, we were invited to write a review article on the use of hybrid yeasts in brewing for Applied Microbiology and Biotechnology, and I’m happy to say that the article has been published online now. In it we sum up the research that has been done on the use of artificial or de novo yeast hybrids for brewing applications, and discuss what kind of benefits they have to the process. These include creating strains with improved aroma formation, fermentation rate and stress tolerance. There is also a short section on how to create these hybrids. Feel free to have a look if you are interested, the article is open access!

The natural interspecies Saccharomyces cerevisiae × Saccharomyces eubayanus hybrid yeast is responsible for global lager beer production and is one of the most important industrial microorganisms. Its success in the lager brewing environment is due to a combination of traits not commonly found in pure yeast species, principally low-temperature tolerance, and maltotriose utilization. Parental transgression is typical of hybrid organisms and has been exploited previously for, e.g., the production of wine yeast with beneficial properties. The parental strain S. eubayanus has only been discovered recently and newly created lager yeast strains have not yet been applied industrially. A number of reports attest to the feasibility of this approach and artificially created hybrids are likely to have a significant impact on the future of lager brewing. De novo S. cerevisiae × S. eubayanus hybrids outperform their parent strains in a number of respects, including, but not restricted to, fermentation rate, sugar utilization, stress tolerance, and aroma formation. Hybrid genome function and stability, as well as different techniques for generating hybrids and their relative merits are discussed. Hybridization not only offers the possibility of generating novel non-GM brewing yeast strains with unique properties, but is expected to aid in unraveling the complex evolutionary history of industrial lager yeast.

As I’ve mentioned previously in many past posts (e.g. here, here and here), I’m working with and researching the properties of newly created lager yeast hybrids (for my PhD project). In the linked posts, you can read about some of our initial results from the project. These mainly established the technique and showed that de novo lager hybrids can exhibit hybrid vigor over their parent strains. Since then I’ve been looking more closely at how hybrids made from the same parent strains, but with varying ploidy levels (i.e. chromosome numbers), behave in regards to fermentation performance, aroma compound production and stress tolerance. We had some very interesting results, and we saw (at least with our hybrids) that the hybrids with higher ploidy level performed better and produced more aroma-rich beer. In order to try to understand why, we sequenced the hybrids and performed transcriptional analysis on selected genes. We saw that the higher ploidy hybrids had higher copy numbers of several genes related to aroma synthesis, and these were also transcribed at higher levels during fermentation. I held a presentation about this research at the 5th International Young Scientists Symposium on Malting, Brewing and Distilling in Chico about a month ago. You can download the presentation slides below! I’m also very happy to announce that we recently had a manuscript on this work accepted for publication in Applied Microbiology and Biotechnology. ‘Ploidy influences the functional attributes of de novo lager yeast hybrids‘ was just published online, and you can find a link to the publication below as well (it is Open Access!).

The genomes of hybrid organisms, such as lager yeast (Saccharomyces cerevisiae × Saccharomyces eubayanus), contain orthologous genes, the functionality and effect of which may differ depending on their origin and copy number. How the parental subgenomes in lager yeast contribute to important phenotypic traits such as fermentation performance, aroma production, and stress tolerance remains poorly understood. Here, three de novo lager yeast hybrids with different ploidy levels (allodiploid, allotriploid, and allotetraploid) were generated through hybridization techniques without genetic modification. The hybrids were characterized in fermentations of both high gravity wort (15 °P) and very high gravity wort (25 °P), which were monitored for aroma compound and sugar concentrations. The hybrid strains with higher DNA content performed better during fermentation and produced higher concentrations of flavor-active esters in both worts. The hybrid strains also outperformed both the parent strains. Genome sequencing revealed that several genes related to the formation of flavor-active esters (ATF1, ATF2¸ EHT1, EEB1, and BAT1) were present in higher copy numbers in the higher ploidy hybrid strains. A direct relationship between gene copy number and transcript level was also observed. The measured ester concentrations and transcript levels also suggest that the functionality of the S. cerevisiae– and S. eubayanus-derived gene products differs. The results contribute to our understanding of the complex molecular mechanisms that determine phenotypes in lager yeast hybrids and are expected to facilitate targeted strain development through interspecific hybridization.

Screening for the brewing ability of non-Saccharomyces yeasts by Maximilian Michel

Maximilian talked about the use of non-conventional yeasts for beer production and he had screened a range of non-Saccharomyces yeasts for brewing potential. Yeast isolates were first identified with genetic fingerprinting and RT-qPCR, and then sent through an initial screening test, which included growth on various carbon sources (glucose, fructose, sucrose, maltose, maltotriose and melibiose), hop resistance (various concentrations of iso-alpha acids), ethanol tolerance (various concentrations of ethanol) and phenolic off-flavour production. Promising strains were then chosen for 2L fermentations. He had focused especially on Torulaspora delbrueckii (but he had also looked at Schizosaccharomyces pombe, Pichia anomala, Hanseniaspora uvarum, Kluyveromyces lactis and Kluyveromyces marxianus), and out of the ten strains he had fermented with at ‘larger’ scale, only one was able to use maltose (and maltotriose). That strain also produced a fruity and berry-like flavour profile. So there are definitely gems to be found in the vast range of wild yeast that are available in nature.

Lachancea thermotolerans in primary beer fermentations by Jen House

Jen continued on the topic of using wild yeast in beer fermentations. Her research was on the use of Lachancea thermotolerans, which is an interesting species because of its ability to produce lactic acid. Hence, there is potential to use it in pure culture fermentations for the production of sour beer. Jen had tested three different strains of various origins in wort fermentations, and found that all three were able to use maltose, but not maltotriose. The three strains also produced more lactic acid and glycerol than the S. cerevisiae control. They also seemed to have quite low O2 requirements and were resistant to iso-alpha acids up to at least 60 IBU, which makes them interesting for brewing use. The pH only dropped to around 4.2 in her experimental fermentations, which means that they will only produce a mildly tart beer and may not be suitable for sour beers (as the only microbe). Lachancea yeasts have been isolated from the bark of oak trees, so that may be a good place to start looking in case you are interested in trying to isolate your own!

Emile has been looking at the biodiversity of Beninese sorghum beers by isolating yeasts and lactic acid bacteria from starter cultures brought from Benin. These starter cultures aren’t made from pure yeast cultures, rather a small amount of beer from the previous batch is used as a starter culture for the next. Emile had isolated (identification by ITS-PCR and MALDI-TOF-MS) a range of yeasts (e.g. Saccharomyces cerevisiae, Candida krusei, Candida ethanolica and Debaryomyces hansenii) and lactic acid bacteria (Lactobacillus plantarum, Lactobacillus fermentum, Lactobacillus helveticus, Lactobacillus brevis and Lactobacillus paracasei) from a starter culture, and he further screened these for the ability to use various carbon and nitrogen sources, as well as beta-glucosidase ability (in order to break down the cyanogenic compound dhurrin that is found in sorghum). Several possible candidate isolates were identified and these are to be used in some pilot-scale fermentations next. Again shows how much ‘wild’ microbes are out there that are potentially useful in brewing!

Invited Speaker: Yeast culture collections by Kyria Boundy-Mills

This talk was a bit different, as Kyria talked about the Phaff yeast culture collection (of which she is the curator of). The Phaff collection is the fourth largest in the world, and contains thousands of yeasts. Many of the deposited yeasts have not been characterized very well, so Kyria talked about the possibility of finding ‘hidden gems’ in the collection. These could have some very interesting properties and phenotypes, relevant not only to the brewing industry, but also e.g. the biofuel industry (oleaginous yeast).

Relationships between the speed of fermentation and levels of flavor compounds post-fermentation by Maria Josey

Maria had examined the beer aroma compounds and modelled the fermentation kinetics (using a logistic model) of 10 successive fermentations using serially repitched yeast. The 10 fermentations all behaved quite similarly, with only minor differences in fermentation rate. There also didn’t seem to be any relationship between fermentation rate and number of times the yeast was repitched. This shows that you can easily reuse your yeast for over 10 generations without any significant effects on your fermentation (as long as your hygiene practices are good). Positive linear correlations were found though between the concentrations of several aroma compounds and the maximum fermentation rate (the B parameter in the model). Faster fermentation leads to more isoamyl acetate, isobutyl acetate, ethyl hexanoate and ethyl octanoate, which of course is something that seems logical as these compounds are synthesized from metabolic intermediates.

Jinjing had studied the yeast responses associated with autolysis by performing proteomic and transcriptomic analysis on yeast strains with different tendencies to autolyse. She also presented various methods for the quantification of autolysis, including measuring total protein in beer, the stability of the redox potential and nucleic acid release. Using microarray analysis they had identified a range of genes that were down- and upregulated in yeast strains that showed high tendency for autolysis (e.g. RLM1 and UBC4). To confirm the roles of RLM1 and UBC4 in the autolysis process, these genes were both knocked out and overexpressed in a production strain. Overexpression of RLM1 and knocking out UBC4 led to increased autolysis. However, one must keep in mind that autolysis is a complex process that is influenced by a range of cell functions and genes.

Energy state model for bottling plants by Isabel Osterroth

Isabel held the only presentation in the ‘Packaging’ topic, and she talked about an energy state model which she had developed for bottling plants. Sustainability and reducing energy use, combined with the fact that bottling plant models haven’t been made before, was the driving force for creating the model. The model described the energy use of various machines in the bottling plant depending on their operational state (machines use energy even when idle). A model that was able to predict the energy use of all the separate functions in the bottling plant was successfully created, and future work will include the use of the model for optimization purposes.

Impact of ascorbic acid additions in mashes by Joe Williams

Joe talked about his research on supplementing ascorbic acid to the mash, and gave a virtual tour of the pilot brewery at UC Davis. The motivation for adding ascorbic acid to the mash was to increase thiol and polyphenol formation and to decrease color development in the wort. The study was very preliminary at the moment, and it will be interesting to see the final results. The pilot brewery at UC Davis was quite impressive, featuring a six-vessel 170L brewhouse and four 20L nano-breweries. I am quite jealous.

Kaylyn talked about the use of various glycosidic enzymes in dry hopped beer in order to release glycosidically bound aroma compounds. She had tested a range of commercial Rapidase enzymes and what effect they had on the concentrations of various hop aroma compounds in a beer dry hopped with Cascade. The addition of these enzymes seems to have had quite little effect on linalool concentrations, but the concentration of geranyl acetate seems to have been enhanced with the ‘Rapidase Hoptimase’ enzyme. Their sensory panel also noticed an increase in ‘tropical fruit’-like aroma, which could be attributed to several compounds that weren’t quantified in this experiment. It seems like an interesting idea though; using e.g. Cascade in combination with a glycosidic enzyme to replicate the aroma profile of some of the modern aroma hops (e.g. Citra). Not sure how economical such a solution is though?

Investigating sources of variation during dry-hopping by Daniel Vollmer

Daniel talked about methods to reduce the amount of variability between replicates in dry hopping experiments. Daniel had noticed in earlier experiments that there was quite large variation between his replicates during dry hopping experiments at pilot-scale, and thus attempted to locate sources for this variation. One of the key findings was that oxygen pickup has a large (negative) effect on hop aroma intensity, and this seemed to have been one of the largest sources of variation. Other sources was the raw material (i.e. the hops cones), which for future experiments will be ground. Another interesting observation, which I mentioned already in the summary of Tom Shellhammer’s keynote lecture, was that there is huge variability in oil content within the same hop cultivar (e.g. Cascade) from different farms. Also very interesting, as I mentioned, was that there seemed to have been no correlation between oil content and aroma intensity. So there are clearly other factors that affect hop aroma intensity as well.

I apologize again for the inactivity on the blog. I haven’t been brewing much the last half a year. The wife and I bought a house in the end of last year and we’ve been renovating it since. We finally moved in a couple of weeks ago, and have started settling in. So soon I’ll be able to return to brewing again! Anyways, last week I attended the 5th International Young Scientists Symposium on Malting, Brewing and Distilling, which was arranged at Sierra Nevada’s brewery from April 21-23, 2016 in Chico, California, USA. First of all I want to thank Ken Grossman, Sierra Nevada, Charlie Bamforth and all the other organizers for a fantastic conference (especially Sierra Nevada for their generosity)! The conference featured great scientific and social program, awesome food, a relaxed atmosphere, amazing people and delicious beer! I myself presented some of the recent research we’ve been conducting on lager yeast hybrids at VTT the past year (I’ll post a link to the presentation slides soon!). To sum up, we’ve been looking at how the ploidy of new lager yeasts affect their phenotypical properties. I’ll be writing up a more detailed post on this particular research soon, as we just had a manuscript on this work accepted.

As I mentioned, there were a lot of interesting presentations during the conference! I thought I’d write some short notes / summaries of all the presentations in case you are interested. Since there were a lot of presentations, I’m splitting this post into three parts. Anyways, here is the first third of the summaries:

Keynote: How Craft Brewing is Transforming the Way We Think About Hops and Hop Flavor by Tom Shellhammer

Tom opened the conference with an interesting talk on the current situation of hop use in the craft industry and hop research at OSU. Craft brewers are using more and more of the global hop production, which also has shifted from being ‘bitter hop’-dominated to being ‘aroma hop’-dominated. Tom also reminded the audience that 1 IBU is not the same as 1 ppm iso-alpha acid. This is particularly relevant with heavily dry hopped beers, where oxidized alpha acids (which are bitter, but not as bitter as iso-alpha acids) can influence the IBU value. In some commercial (dry hopped) beers that had been analysed at OSU, they had observed very high levels of oxidized alpha acids. Another point that was brought up, was that the perceived bitterness gets saturated at high IBU levels (i.e. very little sensorial difference between a 80 IBU beer and a 100 IBU beer). Tom also showed a very interesting figure (which Daniel Vollmer showed again later in his presentation), showing the relationship between hop oil content in Cascade hops sourced from different farms and the hop aroma intensity in beers brewed with these hops (determined by a sensory panel). What was extremely interesting was that there seemed to be no correlation what so ever. The beer brewed with the Cascade hops with lowest oil content actually seemed to have one of the highest aroma intensities. Furthermore, many of the Cascade hops that had the highest oil contents produced beers with the lowest aroma intensities. This just shows that blindly looking at hop oil contents in hops doesn’t actually tell very much about what kind of hop aroma it will give to the beer. If I remember correctly, Tom also suggested that there was no correlation between linalool or myrcene concentrations and the hop aroma intensity either, meaning that there are other key aroma compounds responsible for hop aroma out there that still need to be identified.

Towards the release of a 2-row barley variety for California craft malting and brewing by Joshua Hegarty

Joshua talked about how they have attempted to breed a 2-row barley variety that would be suitable for the ‘harsh’ growing conditions in California. These include an abundance of plant pathogens and dry conditions. They had crossed different parent strains, and selected superior varieties which they had then tested in the field. The new breeding lines had shown good yields and malting quality in the field trials. Using gene mapping they had also found several regions associated with disease tolerance in barley.

Impact of barley varieties on malt and beer flavor by Lindsay Barr

Lindsay presented some research on the influence of barley varieties on malt and beer flavour that had been carried out at the New Belgium Brewing. Barley variety seems to have quite a big influence on both wort and beer flavour (at least according to their sensory panel). However, there didn’t seem to be any correlation between the flavours that were observed in the wort and the beer. Beer age seemed to have had a bigger impact on the beer flavour than the barley variety.

Katy talked about some of the hop-related research that had been done at Sierra Nevada Brewing. Her background was in environmental chemistry, where she had used different extraction methods to quantify hydrocarbons from environmental samples. Here, she talked about how they had tested two different extraction methods, selective pressurized liquid extraction and Likens Nickerson distillation, to test the efficiency of their hop torpedo. Both methods seemed to have yielded quite similar results for some of the compounds that were analysed. However, the main points that were brought up were that the extracted amount does not equal the actual contents and subsequently the importance of good internal standards (that behave chemically and physically as similarly as the compound of interest as possible).

Pro-oxidative effects on the storage stability of German Perle and Czech Saaz pellet hops by Mark Zunkel

Mark had compared the stability of Perle and Saaz hops exposed to oxygen at room temperature during a 9 month period. The hop storage index (HSI; which measures the loss of alpha and beta acids spectrophotometrically) of Perle remained quite stable for around 4 months, after which there was a more rapid loss of the hop acids. Saaz seemed to have remained slightly more stable than Perle, but also experienced a more rapid loss in the latter half of the experiment. Unsurprisingly, both hop varieties suffered a rapid loss of hop oil in the pro-oxidative environment (50% loss of hop oil in a week). This just shows that aroma hops should be stored cold and without the presence of oxygen!

The effect of hopping regime, cultivar and yeast ß-glucosidase activity on terpene alcohol levels in beer by Daniel Sharp

Daniel talked about the research he had been doing on the release of hop terpenes into beer from hop glycosides. This is an interesting topic for brewers interested in hop aroma, as aroma-active compounds can potentially be released during fermentation through the hydrolysis of hop-derived glycosides in the beer. He had tested the beta-glucosidase activity of a wide range of brewing yeast strains, and then selected strains with high and low activity. Surprisingly, beta-glucosidase activity didn’t seemed to affect the maximum hydrolysis level that was achieved during fermentation (and this level was much lower than the positive control where purified enzyme was added to wort). It just took a slightly longer time to reach this level with the low activity strain. Daniel didn’t seem to see any correlation between beta-glucosidase activity and the amount of aglycones in the beer. Higher glycoside extraction was achieved with whirlpool and dry hopping compared to kettle hopping. Some varieties that seemed to be high in glycosides were Columbus, Centennial, Simcoe and Summit.

Margaux talked about her MSc project, which was carried out as a collaboration between Edinburgh Gin and ICBD. During the project, she and 3 other students had developed a gin featuring Scottish (coastal) botanicals. They went to the Scottish coast to forage for interesting botanicals, and then distilled them in lab scale to develop a recipe. The recipe was then used at larger scale at the distillery to produce a commercial product. One botanical in particular, Bladderwrack, seemed to have given off a strong ‘fishy’ aroma during distillation, and its volatile aroma compounds were analysed in more detail. We later got to try the actual gin, and it was really nice (not at all as salty or ‘fishy’ as I first was expecting). Thanks Margaux!

Katherine talked about some of the research she has been doing the last 15 years. This research has been focused mainly on repitching, yeast viability, stress tolerance and petite mutants. Most interesting to me was the work on why ‘1st Generation’ yeast (i.e. yeast that have already undergone one fermentation) seem to start fermentation faster than ‘0 Generation’ yeast (i.e. yeast that come straight out of the propagator). One cause, is that G1 yeast bud faster than G0 yeast (i.e. enter the replication cycle faster) and (if I remember correctly) are able to use glucose faster from the wort. G1 yeast also seem to use less FAN from the wort, which I found interesting (less nitrogen demand or more biosynthesis?). They had also used high-throughput screening systems to isolate osmo- and ethanol tolerant strains. A quite interesting remark was that strains are seldom good at both, i.e. an osmotolerant strain is rarely ethanol tolerant as well. One good point that was made regarding these high-throughput systems is that you find what you are looking for. These isolates may have high tolerance, but may otherwise perform badly in wort or produce off-flavours.

Congratulations to Stephen for winning the Cambridge Prize! Stephen talked about the research he had carried out, which won him the Cambridge Prize. His research was focused on petite (or respiratory-deficient) mutants in brewing, and during his presentation he also talked about various stresses the yeast are subjected to during fermentation. Petite mutants (i.e. cells with damaged mitochondrial DNA) form during fermentation as a result of fermentation stresses, and these can accumulate when yeast is repitched for several generations. These petites perform worse in several regards compared to wild type cells, so their accumulation is not desirable from a brewer’s point of view. Some interesting points that were brought up, were that older cells (i.e. cells with more budding scars) were more susceptible to petite formation and that lower mtDNA copy numbers actually didn’t increase the likelihood of petite formation (e.g. older cells tend to have more mtDNA copy numbers). This seems to suggest that the accumulation of mtDNA damage has a higher impact on petite formation than the copy numbers of mtDNA. This was a very interesting talk, and the topic still seems to be quite poorly understood. It will be interesting to follow the topic in the future.

As I mentioned in my previous blog post, I brewed two batches of beer to my friends’ wedding that took place two weeks ago. Today I thought I’d finally write some tasting notes in case someone is interested in trying the recipes. I’m slightly more happy with the Pale Ale, but I have brewed the recipe (or at least variations of it) several times. Both beers were good though! Let’s start with the Dunkel!

The beer pours with a light brown color and it is slightly hazy. The color was a bit lighter than I expected, but then again I didn’t use that much roasted malts in this. A cream colored head is formed, but it collapses quite quickly leaving drapes of lacing along the glass. The appearance is okay. I’m not really sure why it hasn’t cleared despite the 2 months it was lagering in the keg at 0C. The aroma features some light roastiness (hints of dark chocolate), dark fruits, dark malt bread, and syrup/molasses. The aroma is quite clean and promises a malt-forward flavor. The taste is similar to aroma, with a light roastiness and bready malt tones dominating. Towards the end, a slight yeasty fruitiness joins in together with some grassy hops. The finish is quite dry and lightly bitter. Unfortunately the flavour is slightly boozy/solventy as well, which hints that the fermentation was not perfect. It was fermented in a temperature controlled fridge, so perhaps I underpitched or underaerated. The body is on the light side and the carbonation level is a bit too high. It is easy to drink and quite refreshing though. All in all, I’m quite happy, but you can definitely tell that the fermentation didn’t go perfectly. I’ll have to try again next winter.

The Pale Ale was more to my taste, and it was also the beer that got most compliments at the wedding (it also ran out first). It pours with a quite clear golden-amber color (similar to Sierra Nevada’s Pale Ale). This was slightly hazier at the wedding, so it cleared up nicely during two weeks in the fridge. A fluffy white head is also formed during the pour, and it collapses slowly leaving lots of lacing along the glass. A really nice appearance! There is lots of citrus (especially grapefruit), resin and grassy herbs in the aroma. As you can guess, it is very hop forward. The aroma is otherwise very clean and promises a really tasty beer. The taste begins with a slightly sweet caramel cookie flavor, and it is quickly joined by grapefruit and ‘tropical fruit’ hop flavors. Very fruity. The finish ends in a moderate bitterness, that has a slightly grassy and herbal quality to it. Maybe from the dry hops? I remember the beer being grassier at the wedding, so maybe it has cleaned up during these two weeks. The flavor is also very clean, and you can tell the fermentation went well. The beer has a medium body and carbonation level, and is very easy to drink and really refreshing. A really nice APA that suits my taste buds perfectly. It went quickly during the wedding so it seemed like I wasn’t the only one who liked it!

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